Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,906,0360CT54.5% 1.4 / 11.7 11S266S (TCG→TCA) htpXprotease HtpX
Reads supporting (aligned to +/- strand):  ref base C (1/4);  new base T (6/0);  total (7/4)
Fisher's exact test for biased strand distribution p-value = 1.52e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.28e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGCTGGTTGCTTCTTGCGGTTCATAGCTGGTTTTCAGGCGCTGCA  >  NZ_CP009273/1905952‑1906109
                                                                                    |                                                                         
ttACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACtt                                                                      <  1:432499/90‑1 (MQ=255)
      cAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGtt                                                                <  2:301466/90‑1 (MQ=255)
       aGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGGCATTAACAAACCACTGAGCGCTTTTGACCTTCCGCTa                                                               >  2:308910/1‑90 (MQ=255)
       aGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAAAAACTCACCGAGCGATTTTGACTTAcccgtt                                                               >  2:432499/1‑86 (MQ=255)
             tCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGGGGGGGATGAACAAAACACTGAGCGGTTTTGTCTTACCGTTAATGCag                                                         >  2:420913/1‑90 (MQ=255)
              cACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCaga                                                        <  1:420913/90‑1 (MQ=255)
                          gagCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGc                                            <  2:982/90‑1 (MQ=255)
                          gagCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACTCCCCTAGCGATTTTGACTTTCCGTTAATGCAGAGAGCCATCATGc                                            >  2:521783/1‑90 (MQ=255)
                          gagCTTCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAACAACCCCCTGAGCGATTTTGACTTACCGGTTATGCAGAGAGGCATCATGc                                            >  2:4216/1‑90 (MQ=255)
                              ttCAATTCGTTTATCCAGCGGCGGGGGGGGCATGAAAAACTCACTGAGCGATTTTGACTTTCCCTTTATGCAGAGAGCCCTCATGCTGGt                                        >  2:60749/1‑90 (MQ=255)
                                                                    acTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGCTGGTTGCTTCTTGCGGTTCATAGCTGGTTTTCAGGCGCTGCa  >  2:590895/1‑90 (MQ=255)
                                                                                    |                                                                         
TTACTTCAGGTATTCACCCGTACGCAGAGCTTCAATTCGTTTATCCAGCGGCGGGTGGGTCATGAACAACTCACTGAGCGATTTCGACTTACCGTTAATGCAGAGAGCCATCATGCTGGTTGCTTCTTGCGGTTCATAGCTGGTTTTCAGGCGCTGCA  >  NZ_CP009273/1905952‑1906109

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑